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Structure of the Mycobacterium tuberculosis APS kinase CysC in complex with AMPPNP and APS
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4BZP PDB ENTRY 4BZP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 0.1 M CITRATE, PH 5.3 20% PEG4, 10% 2- PROPANOL, 1.9 MM APS, 2.3 MM AMPPNP, 1.8 MM MGCL2
Crystal Properties Matthews coefficient Solvent content 2.06 40.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.82 α = 90 b = 69.43 β = 90 c = 79.37 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 2011-04-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 ESRF BM14
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.7 49.74 96.6 0.07 11.3 4.3 38074 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.79 83.3 0.52 2.3 3.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 4BZP 1.7 52.26 36095 1930 96.3 0.17619 0.17415 0.1856 0.21599 0.2189 RANDOM
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.736 r_dihedral_angle_3_deg 12.996 r_dihedral_angle_4_deg 12.843 r_long_range_B_refined 6.426 r_long_range_B_other 6.392 r_dihedral_angle_1_deg 5.34 r_scangle_other 4.589 r_scbond_it 3.183 r_scbond_other 3.181 r_mcangle_other 2.745
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.736 r_dihedral_angle_3_deg 12.996 r_dihedral_angle_4_deg 12.843 r_long_range_B_refined 6.426 r_long_range_B_other 6.392 r_dihedral_angle_1_deg 5.34 r_scangle_other 4.589 r_scbond_it 3.183 r_scbond_other 3.181 r_mcangle_other 2.745 r_mcangle_it 2.743 r_angle_refined_deg 2.032 r_mcbond_it 2.018 r_mcbond_other 2.015 r_angle_other_deg 1.294 r_chiral_restr 0.107 r_bond_refined_d 0.019 r_gen_planes_refined 0.012 r_bond_other_d 0.007 r_gen_planes_other 0.007 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2678 Nucleic Acid Atoms Solvent Atoms 173 Heterogen Atoms 203
Software Software Software Name Purpose REFMAC refinement PHASER phasing